I know this probably doesn't count as a bug as the game runs perfectly at native resolution, but when I set the internal resolution to anything higher, there's vertical black lines across the game (with fixed width between each). So far I've seen this happen in Mana Khemia :2 Fall of Alchemy and Mobile Suit Gundam 00: Gundam Meister.
Indeed an annoying problem but there's not much we can do about it.
These are small rounding differences when working with the Direct3D floating point system
versus the all integer based GS coordinate system.
Precise fixes would have to be made for each game right?
That'd reduce the glitches but some floating point rounding problems cannot be solved at all.
There is a workaround to it, some games use 540x540 and that seems to confuse the scaling mechanism, try using 1080x1080, I know for sure it works in some games I have and sadly don't have those you told... still worthy a try.